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Source code for tvb.interfaces.web.controllers.burst.region_model_parameters_controller

# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and 
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
.. moduleauthor:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
.. moduleauthor:: Ionel Ortelecan <ionel.ortelecan@codemart.ro>
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>

"""

import json

import cherrypy
from tvb.adapters.visualizers.connectivity import ConnectivityViewer
from tvb.core.entities import load
from tvb.core.entities.storage import dao
from tvb.core.services.burst_config_serialization import SerializationManager
from tvb.interfaces.web.controllers import common
from tvb.interfaces.web.controllers.autologging import traced
from tvb.interfaces.web.controllers.burst.base_controller import BurstBaseController
from tvb.interfaces.web.controllers.decorators import expose_page, handle_error, check_user
from tvb.interfaces.web.controllers.simulator.simulator_controller import SimulatorWizzardURLs
from tvb.interfaces.web.entities.context_simulator import SimulatorContext


@traced
[docs]class RegionsModelParametersController(BurstBaseController): """ Controller class for placing model parameters in nodes. """ def __init__(self): super(RegionsModelParametersController, self).__init__() self.simulator_context = SimulatorContext() @staticmethod def _dynamics_json(dynamics): """ Construct a json representation of a list of dynamics as used by the js client """ ret = {} for d in dynamics: ret[d.id] = { 'id': d.id, 'name': d.name, 'model_class': d.model_class } return json.dumps(ret)
[docs] def no_dynamics_page(self): params = ({ 'title': 'Model parameters', 'mainContent': 'burst/model_param_region_empty', }) return self.fill_default_attributes(params)
@expose_page
[docs] def index(self): current_user_id = self.simulator_context.logged_user.id # In case the number of dynamics gets big we should add a filter in the ui. dynamics = dao.get_dynamics_for_user(current_user_id) if not dynamics: return self.no_dynamics_page() sim_config = self.simulator_context.simulator connectivity = sim_config.connectivity if connectivity is None: msg = 'You have to select a connectivity before setting up the region Model. ' common.set_error_message(msg) raise ValueError(msg) current_project = common.get_current_project() conn_idx = load.load_entity_by_gid(connectivity) params = ConnectivityViewer.get_connectivity_parameters(conn_idx, current_project.name, str(conn_idx.fk_from_operation)) burst_config = self.simulator_context.burst_config params.update({ 'title': 'Model parameters', 'mainContent': 'burst/model_param_region', 'isSingleMode': True, 'submit_parameters_url': '/burst/modelparameters/regions/submit_model_parameters', 'dynamics': dynamics, 'dynamics_json': self._dynamics_json(dynamics), 'initial_dynamic_ids': burst_config.dynamic_ids }) return self.fill_default_attributes(params, 'regionmodel')
@cherrypy.expose @handle_error(redirect=True) @check_user
[docs] def submit_model_parameters(self, node_values): """ Collects the model parameters values from all the models used for the connectivity nodes. Assumes that the array indices are consistent with the node order. """ dynamic_ids = json.loads(node_values) dynamics = [dao.get_dynamic(did) for did in dynamic_ids] for dynamic in dynamics[1:]: if dynamic.model_class != dynamics[0].model_class: raise Exception("All dynamics must have the same model type") model_name = dynamics[0].model_class burst_config = self.simulator_context.burst_config simulator_config = self.simulator_context.simulator # update model parameters in burst config des = SerializationManager(simulator_config) model_parameters = [dict(json.loads(d.model_parameters)) for d in dynamics] des.write_model_parameters(model_name, model_parameters) # update dynamic ids in burst config burst_config.dynamic_ids = json.dumps(dynamic_ids) # Update in session the simulator configuration and the current form URL in wizzard for burst-page. self.simulator_context.set_burst_config(burst_config) self.simulator_context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_INTEGRATOR_URL) raise cherrypy.HTTPRedirect("/burst/")